The best caulks are the marine grade polyurethanes, not the household silicones sold in the big box stores. Many threads are available for specific products and applications, if you do some searches.

gard

I have a 2000 Sundowner.  The roof caulk was breaking down too.  

The best and easiest method of removing the old caulk is a knife to cut the majority off.  Then use a wire brush wheel in as powerful a side grinder or drill you can get.  The wire brush leaves a clean metal surface for the new caulk.

Sundowner uses this caulking on the exterior of their trailers.  It's very durable.

The caulk used is a moisture cured polyurethane.  Manufactured by Sika Corp.

30800 Stephenson highway

Madison Heights, MI  48071, 248-577-0020

The name is Sikaflex - 221 SF, Product code is 220-242

The OEM color  used is "AL Gray"

 You might also try marine / boat supply as a place to purchase it too.

Couple of tips ...

use masking tape on the roof to keep the caulk line neat.  Pull the tape before the caulk sets hard or the caulk will hold the tape.

An old credit card makes a fair tool to smooth the caulk line evenly. Squeeze the edges of the card to create a curved shaper.